Rivers and wetland ecosystems are degraded by diversions of water upstream. In response, governments have reallocated water to flood wetlands, mimicking natural inundation of habitats known to drive booms in native freshwater fish production. Individual flow events allow the influences of various factors on the ecological outcomes of restoration efforts to be evaluated, in order to improve ongoing adaptive management. This study investigated the population size and recruitment responses of seven native and three alien fish species to widespread floodplain inundation at 15 sites across the Macquarie Marshes, a regulated wetland in Australia’s Murray-Darling Basin. Flooding during late-winter, when water temperatures were 4 to 12.6 degrees C below the spawning threshold for native fish species present in the system, promoted reproduction and recruitment by alien species, which were significantly more abundant than native species after flooding. Fish assemblage structure also differed significantly between main-channel and floodplain habitats, with macrophytes, pH, emergent vegetation, flow velocity and small wood debris accounting for 59% of spatio-temporal variation in fish assemblage structure. Strong correlations were identified between the length of spawning window and post-flood abundance of young-of-year and recruit size classes in the most abundant alien and native fish species. Future environmental flows, particularly those that inundate floodplain habitats, need to be delivered in light of the confounding effects of flow-temperature coupling and the lower spawning temperature thresholds of alien species.